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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SLC12A6
solute carrier family 12 member 6
Chromosome 15 Β· 15q14
NCBI Gene: 9990Ensembl: ENSG00000140199.13HGNC: HGNC:10914UniProt: Q6NSI7
69PubMed Papers
22Diseases
0Drugs
235Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
potassium ion import across plasma membranepotassium:chloride symporter activitymonoatomic ion transportcell volume homeostasisagenesis of the corpus callosum with peripheral neuropathyCorpus callosum agenesis - neuronopathyCharcot-Marie-Tooth disease, axonal, IIa 2IIgenetic disorder
✦AI Summary

SLC12A6 encodes a potassium-chloride cotransporter (KCC3) that mediates electroneutral K+-Cl- symport activated by cell swelling, contributing to cell volume homeostasis 1. The transporter functions across plasma membranes and is involved in ion homeostasis in multiple tissues including red blood cells and nervous system cells 2. Biallelic SLC12A6 mutations cause autosomal-recessive hereditary motor and sensory neuropathy with corpus callosum agenesis (Andermann syndrome), characterized by infantile-onset peripheral neuropathy and central nervous system involvement 3. Heterozygous variants produce dominant Charcot-Marie-Tooth (CMT) disease with remarkable phenotypic heterogeneity depending on specific mutations 4. The Gly552Asp variant causes late-onset, sensory-predominant axonal neuropathy 5, while Arg207His causes severe childhood-onset demyelinating neuropathy 64. Functional studies in Xenopus oocytes demonstrate these mutations significantly reduce potassium influx capacity 56. Clinically, SLC12A6-related CMT presents with variable onset (ages 1-45 years) and severity, with some patients developing intellectual disability or epilepsy alongside neuropathy 7. This phenotypic diversity across different mutations is unprecedented among CMT genes. Genetic screening for SLC12A6 is recommended in CMT patients, particularly those with concurrent central nervous system manifestations 7.

Sources cited
1
SLC12A6 mediates electroneutral potassium-chloride cotransport when activated by cell swelling
PMID: 16048901
2
KCC3 (encoded by SLC12A6) is a major K-Cl cotransporter isoform in red blood cells and other tissues involved in ion homeostasis
PMID: 21733850
3
SLC12A6 mutations cause pediatric neurological disorders and are included in SLC gene variants associated with diverse phenotypes
PMID: 34797406
4
Heterozygous SLC12A6 Gly552Asp variant causes late-onset sensory-motor axonal neuropathy with reduced potassium influx in functional studies
PMID: 36542484
5
SLC12A6 heterozygous variants cause Charcot-Marie-Tooth disease with variable age of onset and can present with intellectual disability and epilepsy
PMID: 35733399
6
Different SLC12A6 heterozygous variants cause CMT with dramatically different phenotypes, severity, and age of onset, representing unprecedented phenotypic diversity for any CMT gene
PMID: 41500801
7
De novo SLC12A6 variants cause dominant CMT; mutant KCC3 shows significantly reduced potassium influx in Xenopus oocyte studies
PMID: 31439721
8
Biallelic SLC12A6 frameshift variants are associated with neurodevelopmental disorders in consanguineous families
PMID: 39281811
Disease Associationsβ“˜22
agenesis of the corpus callosum with peripheral neuropathyOpen Targets
0.82Strong
Corpus callosum agenesis - neuronopathyOpen Targets
0.77Strong
Charcot-Marie-Tooth disease, axonal, IIa 2IIOpen Targets
0.75Strong
genetic disorderOpen Targets
0.47Moderate
Usher syndrome type 1COpen Targets
0.34Weak
peripheral neuropathyOpen Targets
0.34Weak
Agenesis of corpus callosumOpen Targets
0.27Weak
Abnormal facial shapeOpen Targets
0.27Weak
Clinodactyly of the 5th fingerOpen Targets
0.27Weak
HypertelorismOpen Targets
0.27Weak
Low-set earsOpen Targets
0.27Weak
Charcot-Marie-Tooth diseaseOpen Targets
0.18Weak
autosomal recessive axonal hereditary motor and sensory neuropathyOpen Targets
0.11Weak
esophageal squamous cell carcinomaOpen Targets
0.07Suggestive
Charcot-Marie-Tooth disease type 1COpen Targets
0.07Suggestive
Charcot-Marie-Tooth disease type 1AOpen Targets
0.07Suggestive
Charcot-Marie-Tooth disease type 1FOpen Targets
0.07Suggestive
Autosomal dominant intermediate Charcot-Marie-Tooth disease type BOpen Targets
0.07Suggestive
Charcot-Marie-Tooth disease dominant intermediate BOpen Targets
0.07Suggestive
Charcot-Marie-Tooth disease type 4AOpen Targets
0.06Suggestive
Agenesis of the corpus callosum, with peripheral neuropathyUniProt
Charcot-Marie-Tooth disease, axonal, type 2IIUniProt
Pathogenic Variants235
NM_001365088.1(SLC12A6):c.2436+1delPathogenic
Agenesis of the corpus callosum with peripheral neuropathy|Charcot-Marie-Tooth disease|not provided|SLC12A6-related disorder|Agenesis of the corpus callosum with peripheral neuropathy;Charcot-Marie-Tooth disease, axonal, IIa 2II|Melanoma
β˜…β˜…β˜†β˜†2026
NM_001365088.1(SLC12A6):c.2265G>A (p.Trp755Ter)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2026β†’ Residue 755
NM_001365088.1(SLC12A6):c.288dup (p.Ile97fs)Likely pathogenic
Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2025β†’ Residue 97
NM_001365088.1(SLC12A6):c.776del (p.Ala259fs)Pathogenic
not provided|Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2025β†’ Residue 259
NM_001365088.1(SLC12A6):c.316+1G>APathogenic
not provided|Agenesis of the corpus callosum with peripheral neuropathy|Agenesis of the corpus callosum with peripheral neuropathy;Charcot-Marie-Tooth disease, axonal, IIa 2II|Usher syndrome type 1C
β˜…β˜…β˜†β˜†2025
NM_001365088.1(SLC12A6):c.571_572dup (p.Tyr192fs)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2025β†’ Residue 192
NM_001365088.1(SLC12A6):c.1616G>A (p.Gly539Asp)Likely pathogenic
Charcot-Marie-Tooth disease|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 539
NM_001365088.1(SLC12A6):c.3227+1G>ALikely pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|not provided|Agenesis of the corpus callosum with peripheral neuropathy;Charcot-Marie-Tooth disease, axonal, IIa 2II
β˜…β˜…β˜†β˜†2025
NM_001365088.1(SLC12A6):c.2230C>T (p.Arg744Ter)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 744
NM_001365088.1(SLC12A6):c.2437-2A>GLikely pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|not provided|Agenesis of the corpus callosum with peripheral neuropathy;Charcot-Marie-Tooth disease, axonal, IIa 2II
β˜…β˜…β˜†β˜†2025
NM_001365088.1(SLC12A6):c.379G>T (p.Glu127Ter)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|not provided|Agenesis of the corpus callosum with peripheral neuropathy;Charcot-Marie-Tooth disease, axonal, IIa 2II
β˜…β˜…β˜†β˜†2025β†’ Residue 127
NM_001365088.1(SLC12A6):c.2002C>T (p.Arg668Ter)Pathogenic
not provided|Agenesis of the corpus callosum with peripheral neuropathy|Charcot-Marie-Tooth disease, axonal, IIa 2II;Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2025β†’ Residue 668
NM_001365088.1(SLC12A6):c.752dup (p.Ser252fs)Pathogenic
Hypertelorism;Corpus callosum, agenesis of;Clinodactyly of the 5th finger;Abnormal facial shape;Low-set ears|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 252
NM_001365088.1(SLC12A6):c.2809C>T (p.Arg937Ter)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 937
NM_001365088.1(SLC12A6):c.963C>A (p.Tyr321Ter)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 321
NM_001365088.1(SLC12A6):c.1118+1G>APathogenic
Agenesis of the corpus callosum with peripheral neuropathy|Charcot-Marie-Tooth disease|not provided
β˜…β˜…β˜†β˜†2025
NM_001365088.1(SLC12A6):c.2971A>G (p.Thr991Ala)Likely pathogenic
Charcot-Marie-Tooth disease, axonal, IIa 2II|not provided|Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2024β†’ Residue 991
NM_001365088.1(SLC12A6):c.1655G>A (p.Gly552Asp)Pathogenic
not provided|Peripheral neuropathy|Charcot-Marie-Tooth disease, axonal, IIa 2II
β˜…β˜…β˜†β˜†2024β†’ Residue 552
NM_001365088.1(SLC12A6):c.745+2T>APathogenic
Agenesis of the corpus callosum with peripheral neuropathy|not provided
β˜…β˜…β˜†β˜†2024
NM_001365088.1(SLC12A6):c.3031C>T (p.Arg1011Ter)Pathogenic
Agenesis of the corpus callosum with peripheral neuropathy|See cases|not provided|Charcot-Marie-Tooth disease, axonal, IIa 2II;Agenesis of the corpus callosum with peripheral neuropathy
β˜…β˜…β˜†β˜†2024β†’ Residue 1011
View on ClinVar β†—
Related Genes
STK39Protein interaction92%SLC12A4Shared pathway78%OXSR1Protein interaction74%SPG11Protein interaction71%LGALS9CProtein interaction70%SLC12A1Shared pathway38%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
69%
Lung
50%
Heart
34%
Ovary
21%
Liver
14%
Gene Interaction Network
Click a node to explore
SLC12A6STK39SLC12A4OXSR1SPG11LGALS9CSLC12A1
PROTEIN STRUCTURE
Preparing viewer…
PDB6M22 Β· 2.70 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.62LoF Tolerant
pLIβ“˜
0.01Tolerant
Observed/Expected LoF0.46 [0.34–0.62]
RankingsWhere SLC12A6 stands among ~20K protein-coding genes
  • #6,847of 20,598
    Most Researched69
  • #270of 5,498
    Most Pathogenic Variants235 Β· top 5%
  • #4,353of 17,882
    Most Constrained (LOEUF)0.62 Β· top quartile
Genes detectedSLC12A6
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
1.00
2
SLC gene mutations and pediatric neurological disorders: diverse clinical phenotypes in a Saudi Arabian population.
PMID: 34797406
Hum Genet Β· 2022
0.90
3
Late-onset sensory-motor axonal neuropathy, a novel SLC12A6-related phenotype.
PMID: 36542484
Brain Β· 2023
0.80
4
Novel heterozygous variants of SLC12A6 in Japanese families with Charcot-Marie-Tooth disease.
PMID: 35733399
Ann Clin Transl Neurol Β· 2022
0.70
5
Spectrum of dominant Charcot-Marie-Tooth disease due to
PMID: 41500801
J Neurol Neurosurg Psychiatry Β· 2026
0.60